Added ci for local zipped files (8bc1bca2) · Commits · Chaos / Cutandrun

.github/workflows/ci.yml

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		@@ -33,9 +33,21 @@ jobs:
		wget -qO- get.nextflow.io \| bash
		sudo mv nextflow /usr/local/bin/

		# Work around for the unexpected end of file error that github actions seems to get when downloading compressed files during pipelie
		# execution
		- name: Download data
		run: \|
		wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz
		wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz
		wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz
		wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz
		wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz
		wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

		- name: Run pipeline with test data
		run: \|
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test
		nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip

		##############################
		### LARGE INTEGRATION TEST ###
		##############################

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		@@ -29,7 +29,7 @@ params {
		gene_bed = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz'
		blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
		spikein_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz'
		//spikein_bowtie2 = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'
		spikein_bowtie2 = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'

		minimum_alignment_q_score = 10
		}
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		@@ -17,7 +17,7 @@ params {
		gene_bed = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz'
		blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
		spikein_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz'
		//spikein_bowtie2 = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'
		spikein_bowtie2 = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'

		minimum_alignment_q_score = 10
		}

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		/*
		========================================================================================
		Nextflow config file for running minimal tests
		========================================================================================
		Defines input files and everything required to run a fast and simple pipeline test.

		Use as follows:
		nextflow run nf-core/cutandrun -profile test,<docker/singularity>

		----------------------------------------------------------------------------------------
		*/

		params {
		config_profile_name = 'Test profile'
		config_profile_description = 'Minimal test dataset to check pipeline function'

		// Limit resources so that this can run CI
		max_cpus = 2
		max_memory = 6.GB
		max_time = 6.h

		// Input data
		input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet/test-GSE145187-small.csv'

		// Genome references
		fasta = 'hg38-chr20.fa.gz'
		bowtie2 = 'hg38-chr20-bowtie2.tar.gz'
		gtf = 'hg38-chr20-genes.gtf.gz'
		gene_bed = 'hg38-chr20-genes.bed.gz'
		blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
		spikein_fasta = 'e_coli_U00096_3.fa.gz'
		spikein_bowtie2 = 'e_coli_U00096_3.tar.gz'

		minimum_alignment_q_score = 10
		}
		No newline at end of file